scholarly journals Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex–Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

ACS Omega ◽  
2018 ◽  
Vol 3 (11) ◽  
pp. 14788-14806 ◽  
Author(s):  
Holli-Joi Sullivan ◽  
Carolyn Readmond ◽  
Christina Radicella ◽  
Victoria Persad ◽  
Thomas J. Fasano ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Explicit Solvent ◽  
G Quadruplex ◽  
Dynamics Simulations

Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent

2017 ◽  
Vol 19 (28) ◽  
pp. 18685-18694 ◽  
Author(s):  
Kelly Mulholland ◽  
Farzana Siddiquei ◽  
Chun Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Duplex Dna ◽  
Binding Modes ◽  
Dna Duplex ◽  
Explicit Solvent ◽  
G Quadruplex ◽  
Dynamics Simulations

Binding modes ofRHPS4to DNA duplex and human teloemeric G-quadruplexes from MD simulations.

Prediction of aqueous free energies of solvation using coupled QM and MM explicit solvent simulations

2020 ◽  
Vol 22 (15) ◽  
pp. 8021-8034
Author(s):  
Daniel Sadowsky ◽  
J. Samuel Arey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Energies ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Ionic Solutes

A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water.

scholarly journals Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides

2020 ◽  
Vol 16 (4) ◽  
pp. 2561-2569 ◽  
Author(s):  
Plamen Dobrev ◽  
Sahithya Phani Babu Vemulapalli ◽  
Nilamoni Nath ◽  
Christian Griesinger ◽  
Helmut Grubmüller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Constant Ph ◽  
Explicit Solvent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics
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